This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two implementations of the DER Finder approach are included in this package: (1) single base-level F-statistics and (2) DER identification at the expressed regions-level. The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks.
|Author||Leonardo Collado-Torres [aut, cre], Alyssa C. Frazee [ctb], Andrew E. Jaffe [aut], Jeffrey T. Leek [aut, ths]|
|Date of publication||None|
|Maintainer||Leonardo Collado-Torres <email@example.com>|
analyzeChr: Run the derfinder analysis on a chromosome
annotateRegions: Assign genomic states to regions
calculatePvalues: Calculate p-values and identify regions
calculateStats: Calculate F-statistics at base pair resolution from a loaded...
coerceGR: Coerce the coverage to a GRanges object for a given sample
collapseFullCoverage: Collapse full coverage information for efficient quantile...
coverageToExon: Extract coverage information for exons
createBw: Export coverage to BigWig files
createBwSample: Create a BigWig file with the coverage information for a...
define_cluster: Define a cluster to use.
derfinder-deprecated: Deprecated functions in package 'derfinder'
derfinder-package: Annotation-agnostic differential expression analysis of...
extendedMapSeqlevels: Change naming style for a set of sequence names
filterData: Filter the positions of interest
findRegions: Find non-zero regions in a Rle
fullCoverage: Load the unfiltered coverage information from a group of BAM...
genomeData: Genome samples processed data
genomeDataRaw: Genome samples processed data
genomeFstats: F-statistics for the example data
genomeInfo: Genome samples information
genomeRegions: Candidate DERs for example data
genomicState: Genomic State for Hsapiens.UCSC.hg19.knownGene
getRegionCoverage: Extract coverage information for a set of regions
getTotalMapped: Calculate the total number of mapped reads
loadCoverage: Load the coverage information from a group of BAM files
makeGenomicState: Obtain the genomic state per region from annotation
makeModels: Build model matrices for differential expression
mergeResults: Merge results from different chromosomes
preprocessCoverage: Transform and split the data
railMatrix: Identify regions data by a coverage filter and get a count...
rawFiles: Construct full paths to a group of raw input files
regionMatrix: Identify regions data by a coverage filter and get a count...
sampleDepth: Calculate adjustments for library size